Man page - seqan_tcoffee(1)
Packages contains this manual
- rabema_evaluate(1)
- alf(1)
- mason_materializer(1)
- pair_align(1)
- gustaf(1)
- stellar(1)
- razers3(1)
- sak(1)
- yara_indexer(1)
- mason_frag_sequencing(1)
- micro_razers(1)
- rabema_prepare_sam(1)
- insegt(1)
- rabema_build_gold_standard(1)
- splazers(1)
- seqan_tcoffee(1)
- yara_mapper(1)
- tree_recon(1)
- mason_genome(1)
- mason_methylation(1)
- razers(1)
- snp_store(1)
apt-get install seqan-apps
Manual
SEQAN_TCOFFEE
NAMESYNOPSIS
DESCRIPTION
OPTIONS
Main Options::
Segment Match Generation Options::
Scoring Options::
Guide Tree Options::
Alignment Evaluation Options::
NAME
seqan_tcoffee - Multiple sequence alignment
SYNOPSIS
seqan_tcoffee -s < FASTA FILE > [ OPTIONS ]
DESCRIPTION
SeqAn::T-Coffee is a multiple sequence alignment tool.
(c) Copyright 2009 by Tobias Rausch
OPTIONS
-h , --help
Display the help message.
--version
Display version information.
Main Options::
-s , --seq INPUT_FILE
Name of multi-fasta input file. Valid filetypes are: .frn , .fna , .ffn , .fasta , .faa , and .fa .
-a , --alphabet STRING
The used sequence alphabet. One of protein , dna , rna , and iupac . Default: protein .
-o , --outfile OUTPUT_FILE
Name of the output file. Valid filetypes are: .msf , .frn , .fna , .ffn , .fasta , .faa , and .fa . Default: out.fasta .
Segment Match Generation Options::
-m , --method List of STRING ’s
Defines the generation method for matches. To select multiple generation methods recall this option with different arguments. One of global , local , overlap , and lcs . Default: global and local .
-l , --libraries List of INPUT_FILE ’s
Name of match file. To select multiple files recall this option with different arguments. Valid filetypes are: .mums , .lib , .blast , and .aln .
-pa , --pairwise-alignment STRING
Pairwise alignment method. Default: unbanded for usual alignments (< 50 sequences), banded for deep alignments (>= 50 sequences) One of unbanded and banded .
-bw , --band-width INTEGER
Band width. This option automatically select banded pairwise alignment (see pa for details) In range [2..inf]. Default: 60 .
Scoring Options::
-g , --gop INTEGER
gap open penalty Default: -13 .
-e , --gex INTEGER
gap extension penalty Default: -1 .
-ma , --matrix STRING
score matrix Default: Blosum62 .
-ms , --msc INTEGER
match score Default: 5 .
-mm , --mmsc INTEGER
mismatch penalty Default: -4 .
Guide Tree Options::
-u , --usetree STRING
Name of the file containing the Newick Guide Tree .
-b , --build STRING
Method to build the tree. Following methods are provided: Neighbor-Joining ( nj ), UPGMA single linkage ( min ), UPGMA complete linkage ( max ), UPGMA average linkage ( avg ), UPGMA weighted average linkage ( wavg ). Neighbor-Joining creates an unrooted tree, which we root at the last joined pair. One of nj , min , max , avg , and wavg . Default: nj .
Alignment Evaluation Options::
-i , --infile INPUT_FILE
Name of the alignment file < FASTA FILE > Valid filetypes are: .frn , .fna , .ffn , .fasta , .faa , and .fa .